The advent of DNA sequencing has shown genomes to be one of the most revealing windows onto biological function and evolution at our disposal. For example, in the microbial world, genome sequencing has taught us that lateral gene transfer is a key process responsible for the emergence of virulence and antibiotic resistance, an important and increasing concern in the context of infectious diseases. In response to the enormous diversity of infectious pathogens, in the cells of the immune system, the human genome undergoes a cut-and-paste process that leads to a huge array of unique antibodies. Cells respond to changes in the environment on much faster time scales as well. Different genes are turned on at different times and in different places in response to instantaneous changes in their chemical and physical environment. These regulatory decisions range from the expression of metabolic preferences about which carbon source in an environment to exploit to choices critical to human health, such as whether cells will enter a state of unchecked proliferation or express antibiotic resistance genes. Yet, there remains much that we don't understand about how genomes work. Even in the best understood of organisms such as the bacterium E. coli, we remain completely ignorant of how half of its genes are regulated. Just as protein structures give only a single structural snapshot from a huge array of different conformations, genomes are dynamic too. Further, in analogy with proteins, analysis of sequence is almost never enough to tell us how genes are regulated and exploited in their physiological setting. The research proposed here focuses on three challenging and important aspects of genome dynamics: (i) The use of physical models and single-cell microscopy to develop a mechanistic view of the rules for how genes are transferred between different organisms, a process critical not only to the long-term evolution of microorganisms, but also to the short-term emergence of infectious diseases. (ii) The development of sequencing-based and modeling methods that permit us to determine not only how genes for which we have no regulatory information are regulated, but also to quantitatively characterize their input-output functions. (iii) Quantitative single-cell studies that relate these transcriptional input-output functions to the physiological response of cells to various environmental insults such as antibiotics or osmotic shock. Each of these efforts aims to provide a sequence-level understanding of how genes are transferred, regulated and expressed to carry out physiological functions.